GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Desulfacinum infernum DSM 9756

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  258 bits (659), Expect = 2e-73
 Identities = 149/366 (40%), Positives = 212/366 (57%), Gaps = 29/366 (7%)

Query: 4   IHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRI 63
           I  + + K Y G    +  +   + +G+ +V+LGPSGCGK+T+LR+IAGLE ++ GT+ I
Sbjct: 3   IEIRDVRKDY-GRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHI 61

Query: 64  GGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLN 123
            GT V  LP  +RN++MVFQ+YAL+PH++V +NI FGL+  K PA EI+RR++ V  LL 
Sbjct: 62  AGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLG 121

Query: 124 LEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQR 183
           L   L+ KP  +SGG QQR A+ RAII    V L DEPLSNLDAKLR  +R +I  L +R
Sbjct: 122 LSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRR 181

Query: 184 LRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFL 243
           L  T +YVTHDQ+EAMT+ADR++LM+DG+IVQ  SP   Y  P N F A FIGTP MN +
Sbjct: 182 LGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIV 241

Query: 244 ------SGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPA 297
                  G      G+L          +  +R+            +RP+++R+A   +PA
Sbjct: 242 PLCPTQGGAALEPGGRLLFP------GMDPDRY---------LFGIRPENLRLAESGQPA 286

Query: 298 ASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDV 357
                   V   E LG+D  ++     Q +       R  + G  + L  D  ++++FD 
Sbjct: 287 -------MVTGREYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDA 339

Query: 358 ESGENL 363
            + E +
Sbjct: 340 RTQERV 345


Lambda     K      H
   0.321    0.137    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 391
Number of extensions: 15
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 406
Length of database: 365
Length adjustment: 30
Effective length of query: 376
Effective length of database: 335
Effective search space:   125960
Effective search space used:   125960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory